Hello all,
Just to let you know about a couple of busy periods in the open plan at
YNiC next week. On the 22nd (Wednesday) there will be a group of ~10
school children at YNiC between 14:00 and 15:30 using some of the
machines in open plan. They will be accompanied by a Calendar film crew
so those of you who are camera shy may want to avoid the area.
Alternatively of course, if you want your 5 minutes of fame as
background scientition, feel free to look industrious.
On the 23rd (Thursday, though you probably could have worked that out)
the first of the MSc sessions will be held between 13:15 and 15:15.
During this time open plan will be extremely busy, and there are
unlikely to be machines available. I'd strongly advise you not to come
in to YNiC in the afternoon until after they've finished, when you will
of course be rushing in for the "Taking your research through to
publication" seminar.
Thanks,
Sam
Dear Users
This week's YNiC seminar (4-5 pm) will be given by Piers Cornelissen.
His talk is titled "Virtual electrodes II: an update on group level
analysis of VE data" .
Everyone is welcome to attend.
Best wishes
Rebecca
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Dear Colleagues
The annual user meeting is tomorrow (9th October 2008) at 4pm.
The meeting will be held in the Venables room in Psychology
All welcome
The agenda will be
1. Welcome and statements by the Director (GG)
2. News from YNiC
- The New Science Committee (A. Ellis)
- Ethics & Governance (A. Morland)
- The new database and booking system (YNiC staff)
- Operator training 2008/09 (YNiC staff)
- Proposed changes to web and documentation (YNiC staff)
3. Topics raised by users
- Financial situation at YNiC (GG to lead)
- The proposed charging system (AM to lead)
- The software programme for 08/09 (WW to lead)
4. AOB
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
York
YO10 5DG
tel (+44) (0) 1904 435349
fax (+44) (0) 1904 435356
mobile 07986778954
Dear colleagues
Topics that have been suggested/requested for discussion at the Annual
Users' Meeting, so far, include
a. The financial situation at YNiC (budgets, equipment upgrades,
sustainability)
b. The new booking system
c. Operator training for MRI and MEG (when, how)
d. The proposed charging system for YNiC
e. The software programme (including inclusion of dipole and minimum norm
estimation in the software framework)
f. Ethics and Governance (a proposal for permission to conduct work in an
area rather than by project)
Please do suggest other topics.
We would welcome discussion on the scientific programme at YNiC if Users
would like to suggest specific areas of interest or concern.
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
York
YO10 5DG
tel (+44) (0) 1904 435349
fax (+44) (0) 1904 435356
mobile 07986778954
Dear Users
This week the Thursday afternoon meeting, which will be held in *Venables*
(4-5 pm), is the Annual General Meeting for Users. The purpose of this
meeting is for YNiC staff and Users to discuss the best way forward for
research at YNiC.
Please use ynic-users(a)ynic.york.ac.uk <mailto:ynic-users@ynic.york.ac.uk>
to generate ideas for the agenda.
The co-ordinators for this meeting will be Andy Ellis and Gary Green.
Everyone is welcome to attend.
*N.B. This meeting will be held in Psychology in Venables (room A202)*
--
Dr. Rebecca E. Millman
York Neuroimaging Centre
The Biocentre
York Science Park
York
YO10 5DG
Email: rem(a)ynic.york.ac.uk
Tel: 01904 435 5373
Hello All,
At 4pm today we will be having an informal session on aspects of
neuroimaging that folks picked up at conferences this year. Andre, Michael
and Will are going to give brief talks. I will also be providing some
information concerning the upgrades that will be made at YNiC next week
during the scheduled closure.
As is customary, some light refreshments will be available afterwards.
Hope to see you there
Tony
Antony Morland PhD
Deputy Director York Neuroimaging Centre
Professor of Visual Neuroscience
Department of Psychology
University of York
York YO10 5DD
UK
Tel +44 (0) 1904 432 860
Email a.morland(a)psychology.york.ac.uk
Dear All,
One of the disk partitions used to store analyzed data is full. As an
emergency measure the disk partition is being extended so that analysis
can continue. The extension of the partition will slow access time
considerably this morning, so it would be wise to postpone heavy duty
analysis until this afternoon.
Thanks
Tony
Hello All,
This is a reminder that YNiC will be closed from 5pm Friday 3rd October
through to 9am 13th October for a major infrastructure project. Computing
on the cluster will not be possible during this period and desktop access
will not be available. Cluster jobs submitted on Friday will have to be
complete before 5pm. At 5pm, all cluster jobs will be stopped.
The new infrastructure will allow, among many other improvements,
investigators to book scanner slots via a web interface. Details of the new
booking procedures will appear in another email.
Thanks
Tony
Antony Morland PhD
Deputy Director York Neuroimaging Centre
Professor of Visual Neuroscience
Department of Psychology
University of York
York YO10 5DD
UK
Tel +44 (0) 1904 432 860
Email a.morland(a)psychology.york.ac.uk
This week the Thursday afternoon meeting at YNiC (4-5 pm) will focus on
Users' feedback from conferences that you have attended over the summer.
Everyone is invited to talk about how their neuroimaging work was
received. We would also like to hear about posters/presentations from
other labs that you found particularly interesting and exciting.
Tony Morland will chair this session.Please contact Tony
<a.morland(a)psychology.york.ac.uk> if you would like to contribute.
--
Dr. Rebecca E. Millman
York Neuroimaging Centre
The Biocentre
York Science Park
York
YO10 5DG
Email: rem(a)ynic.york.ac.uk
Tel: 01904 435 5373
Dear Users
Please find below the schedule for YNiC's Thursday sessions (4-5 pm at
YNiC, except where stated).
Please contact me if you have any questions.
Best wishes
Rebecca
*****************************************************************************
2nd October: Debrief from conferences
All Users are invited to talk about how their neuroimaging work was
received at conferences they attended over the summer. We would also
like to hear about posters/presentations from other labs that you found
particularly interesting and exciting. Tony Morland will chair this
session. Please contact Tony Morland <a.morland(a)psychology.york.ac.uk
<mailto:a.morland@psychology.york.ac.uk>> if you would like to contribute.
9th October: Annual User Meeting
A meeting for YNiC staff and Users to discuss the best way forward for
research at YNiC. Please use ynic-users(a)ynic.york.ac.uk
<mailto:ynic-users@ynic.york.ac.uk> to generate ideas for the agenda.
The co-ordinators for this meeting will be Andy Ellis (Chair of Science
Committee) and Gary Green. *N.B. This meeting will be held in Venables
(A202)*
16th October: Analysis Support Colloquium (ASC) - Piers Cornelissen
"Virtual electrodes II: an update on group level analysis of VE data"
23rd October: Taking your research through to publication
This session will focus on problems that YNiC users may be experiencing
in analyzing their data to the point where they are happy to submit it
for publication, and will try to identify issues concerning the analysis
tools, visualisation tools, statistics etc that could usefully be
addressed. Please use ynic-users(a)ynic.york.ac.uk
<mailto:ynic-users@ynic.york.ac.uk> to generate ideas for the agenda.
Gary Green will co-ordinate this meeting.
30th October: External speaker - Joachim Gross
"Oscillatory coupling and activity in sensorimotor areas studied with MEG"
http://www.psy.gla.ac.uk/staff/index.php?id=JG001
6th November: External speaker - Stephan Moratti
"Steady state visual evoked potentials/ fields: Advantages of High
Signal to Noise Ratio in Basic and Clinical Psychophysiological Research"
http://web.mac.com/smoratti/Stephan_Moratti,_Researcher/Stephan_Moratti_Inf…
13th November: Applying for neuroimaging grants
Presentations by Sue Gathercole (and others) on strategies for
successful grant applications.
20th November: TMS lab opening
Silke Goebel and Beth Jeffries will open the new TMS lab.
27th November: Feedback from Annual Users Meeting
Andy Ellis and Gary Green will lead a discussion on the outcomes of the
Annual Users Meeting (9th October).
4th December: Analysis Support Colloquium (ASC) - Silke Goebel
"Investigating Number Processing with MEG - Lost in (Source) Space"
11th December: Work in progress by Users and Staff
Presentations by YNiC staff and Users on current research projects.
Please contact gary.green(a)ynic.york.ac.uk
<mailto:gary.green@ynic.york.ac.uk> if you would like to volunteer.
18th December: Work in progress by Users and Staff (& Christmas
drinks)
Presentations by YNiC staff and Users on current research projects.
Please contact gary.green(a)ynic.york.ac.uk
<mailto:gary.green@ynic.york.ac.uk> if you would like to volunteer.
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Dear all
University Research Committee has delivered its report on YNiC following
the review that was conducted in June. The report compliments YNiC on
having reached the point it has, notes (inevitably) the need for more
external grant income, and makes a variety of points about the
relationship between Psychology and YNiC, the committee structure etc.
that are prefectly acceptable and already being addressed.
The department is required to make a formal response to the review. It
would be good to include in that response the growing list of the
publications that are now emerging from YNiC, along with the conference
presentations.
I attach the most up-to-date list I have. Please could you let me know of
any changes or additions. A response by the end of Friday would be very
helpful.
With thanks
Andy
Simon Duckett and I have organised a chemistry/YNiC hyperpolarisation
team meeting this morning where we are discussing MRI/NMR theory.
As the numbers attending are more than can be housed in my office we are
moving the seminar into the open plan area of YNiC. All are welcome and
the talk will start at 9.30
A presentation on the mathematical background to NMR and MRI will be
presented. The talk will be mainly on Density matrices, Product
operators and the theory behind double quantum states selection in
polarised molecules.
Sorry for the late notice
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
Hello All,
For the start of the new academic year we're making changes that will
require some downtime on the systems here at YNiC. The reason for this
downtime is that we will be implementing some major changes to the
software that helps us run and administer the Centre. Hopefully many of
these changes will go unnoticed, but there will be one or two things
that we hope will make your lives easier. The most significant change
will be the introduction of a new booking system that can be accessed
off site and will allow users to make their own bookings for MRI, TMS
and MEG. This will be part of a new and improved database that will also
allow investigators to track their projects' progress and help us ensure
that the right projects get the appropriate support at the appropriate
time. The upgrades will also include a uniform login and security
system across all the computers (this will be invisible to most users
but does have some major advantages) and a better, more equitable use of
quotas on the filesystems. We will also add more disc space to help with
the current overloading of the existing systems. To do all this we need
to change the servers that run the whole system.
As a result, YNiC will be closed from 5:00 p.m. on Friday the 3rd of
October and will reopen at 9:00 a.m. on Monday the 13th of October.
This version of the database will be released as v0.9, and we already
have some ideas about what will be going into v0.95 and v1.0, but early
next term, when people have had a chance to play with it, we'll be
asking for your input on additional functionality that you'd find
useful. Look out for the Annual Users' Meeting that will provide an
opportunity for users to contribute to planning the next stages of
development.
We will need some additional information for some projects to allow
investigators to take advantage of the new booking procedure, and in the
next couple of days principal investigators will be getting an email
requesting those details. It is very important that we get this
information by the end of the month or some projects will no longer be
able to book time on the scanners.
One unfortunate side effect of some of the changes is that all passwords
will have to be reset. First thing on Monday the 13th when we reopen,
new passwords will be provided which will enable you to login and reset
you password to something more memorable. Hopefully though, that will be
the only disruption and from the 13th normal (and improved) service will
resume.
So, to reiterate, YNiC will be closed between:
17:00 Friday 3rd October and
09:00 Monday 13th October.
If you have any questions about these changes, please contact Sam
Johnson <sam.johnson(a)ynic.york.ac.uk> or Mark Hymers
<mark.hymers(a)ynic.york.ac.uk>.
Thanks, and sorry for any inconvenience,
Sam
Dear colleagues
I am sorry to have to report that MEG is not available due to another,
different, fault.
4D Neuroimaging will be on site tomorrow (Thursday) and will replace a
set of electronics.
I will report when it is available again.
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
Dear Users
I am sorry to have to tell you that MEG is down.
We have an intermittent fault that causes the system to fail such that
either the coil information cannot be captured and/or the channels all
flat line.
We have worked with 4D all week to try and isolate the cause of the
fault but it appears that whatever it is creates a variety of different
fault conditions depending on where in the process stream one has
reached. It is likely that it is due to a processor board problem in the
DAS rack.
4D will be arriving early next week to rectify the matter and will be
replacing a number of cards in the main acquisition rack (the DAS).
I am very sorry for the serious disruption this is causing some of you
at such a critical time in your research studies.
As soon as MEG is available again I will email you.
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
The Canon printer is now back in operation. It should be used for
printing documents that for some reason cannot be read on screen.
Please note that it is not to be used for thesis printing. Students are
responsible for the cost of printing their reports and downloaded
scientific papers.
Please do not use the Xerox printer. This costs more than 50p per sheet!
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
I am sorry to have to report that the printer at YNiC (Canon) has jammed
and is out of operation until an engineer can visit.
I will inform you when it becomes available again
Gary
--
Gary Green
York Neuroimaging Centre
The Biocentre
York Science Park
Innovation Way
Heslington
York
YO10 5DG
http://www.ynic.york.ac.uk
tel. 01904 435349
fax 01904 435356
mobile 07986 778954
Dear all,
an interesting and brief article on the relationship between fMRI and
electrophysiology.
http://dx.doi.org/10.1016/j.cub.2008.03.042
Michael
--
Dr Michael Simpson
Science Liaison Officer
York Neuroimaging Centre
Innovation Way
York
YO10 5DG
Tel: 01904 567614
Web: http://www.ynic.york.ac.uk
Dear users
TAKE HOME MESSAGE: A FRONT-SILVERED MIRROR HAS NOW BEEN MOUNTED IN MRI
IMPROVING IMAGE QUALITY
Many of you will be aware that the visual stimulus delivery setup in
MRI relies on back-projection onto a screen which the participant then
views via a mirror mounted in front of their face.
We have always been aware that standard mirrors are sub-optimal for this
type of setup: as soon as a standard mirror is tilted internal
reflection and refraction of light causes slight blurring of the image
.. sometimes this is perceived as a 'double edge' when viewing object
binocularly.
This effect can be minimised by using a minimum glass thickness in front
of the reflective surface of the mirror. Thus, to date, we have used a
2mm thick mirror to aid image quality. Unfortuantely many of you have
expressed concerns that this is still not as good as you would like.
We have thus decided to fit a custom cut front-silvered mirror in place
of the previous setup. These mirrors have effectively no glass thickness
since it is the front surface of the mirror that is the reflective one.
This (for the money) is as close as we can get to perfect reflection and
should resolve your problems.
Unlike standard mirrors, front-silvered ones have no protection of the
reflective surface and are highly sensitive to scratching and marking.
The mirror can only be cleaned of dust with special products and oily
stains may be impossible to remove. As such all users / operators must
avoid handling the mirror surface directly and should place the mirror
array in place / store with care to avoid scratching of the mirror
surface by other objects.
We hope the improved quality will benefit us all.
Contact me if you have any queries.
Kind regards,
Andre'
--
************************************************************************
Andre Gouws
User Support Manager
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 435328
Fax: +44 (0) 1904 435356
Dear users,
Thanks for reading!
I am a new user about freesurfer, after learning it a little while, I
have got some problems:
1. I have used "recon-all" successfully to process the sMRI data, which
generated the "lh.pial". And, I used "mris_convert lh.pial lh.pial.asc",
get text mesh "lh.pial.asc". May I ask how can I view this with visible
mesh associated with the vertices and triangle?
2. I have read the Manual v 0.8. It seems all of the interface has not
supported in our new Freeserfer version...do you have some good
suggestion about the materials for beginner to learn?
I really appreciate your help!Looking forward to your reply!
Kind regards,
Jing
*N.B. Today's seminar will be held in A202 in Psychology and not in YNiC*
Dear Users
Today's seminar (Thursday 4 pm in the Venables room, A202 ) will be
given by Ole Jensen from FC Donders.
http://oase.uci.ru.nl/~olejen/
The title of his talk will be "How slow event-related fields are created
from cognitive modulations in oscillatory brain activity".
Everyone is welcome to attend and there will be wine and soft drinks
available after the talk.
Best wishes
Rebecca
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Dear Users,
Concatenation or higher level stats?
We would value the input of any users who have experience of 'combining'
fMRI data across multiple runs for more robust averaging.
The issue arises when trials of an experient are acquired in different
data blocks due to technical limitations of scan scquisition protocols or
often to reduce the strain on participants in a single session.
I have searched many available resources. There are well documented
routines for (1) analysinng the sessions individually and then compring
them with a higher level analysis or (2) demeaning the two timeseries and
combining them into a single one .. then following the standard analysis
individual subject routine.
Comments would be appreciated (especially from anyone has first hand
experience of doing this).
Thanks
Andre'
Dear Users
Please note that, contrary to the email I sent this morning, this week's
YNiC seminar will be held in Psychology i.e. *NOT YNIC*.
Ole's talk will be in the Venables room (A202) since B020 is being used
for a graduation party.
Best wishes
Rebecca
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Dear Users
This week's seminar (Thursday 4 pm at YNiC) will be given by Ole Jensen
from FC Donders.
http://oase.uci.ru.nl/~olejen/
The title of his talk will be "How slow event-related fields are created
from cognitive modulations in oscillatory brain activity".
Everyone is welcome to attend and there will be wine and soft drinks
available after the talk.
Best wishes
Rebecca
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
